CP_DiffR2: Title

In XiangningXue/CircadianPipeline: What the Package Does (One Line, Title Case)

Title

Description

Title

Usage

CP_DiffR2(
  x,
  method = "LR",
  TOJR = NULL,
  alpha = 0.05,
  nSampling = 1000,
  Sampling.save = NULL,
  Sampling.file.label = "gII_vs_gI",
  p.adjust.method = "BH",
  parallel.ncores = 1
)

Arguments

x	outpuf of CP_Rhythmicity(x1, x2)
method	one of "LR", "permutation", "bootstrap". "LR" is recommended.
TOJR	toTOJR output. If NULL, rhythm.joint object in x will be used.
alpha	cutoff of p-values for significant differential rhythm fitness change.
nSampling	number of samplings if "permutation" or "bootstrap" is chosen for method
Sampling.save	directory to save sampling results. If NULL, the result will not be saved.
Sampling.file.label	character string. Used as file lable if sampling results are saved.
p.adjust.method	input for p.adjust() in R package stat
parallel.ncores	integer. Number of cores used if using parallel computing with mclapply(). Not functional for windows system.

Value

A dataframe of differential rhythm finess test results.

Examples

x = CP_sim_data(ngene=1000, nsample=30, A1=c(1, 3), A2=c(1, 3),
phase1=c(0, pi/4), phase2=c(pi/4, pi/2),
M1=c(4, 6), M2=c(4, 6), sigma1=1, sigma2=1)
rhythm.res = CP_Rhythmicity(x1 = x[[1]], x2 = x[[2]])
rhythm.diffR2 = CP_DiffPar(rhythm.res)

XiangningXue/CircadianPipeline documentation built on May 3, 2022, 3:04 p.m.